Contacts of the strand formed by residues 140 - 152 (chain B) in PDB entry 2IVB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B LYS* 3.2 41.1 + - + +
133B VAL 3.7 6.5 - - - +
134B ALA* 5.2 4.0 - - - -
139B GLY* 1.3 78.1 - - - +
141B ARG* 1.3 56.8 + - - +
116F PHE* 4.4 18.1 - - + +
149F LYS* 3.2 8.4 - - - +
150F TYR* 2.6 59.2 + - + +
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 3.5 1.6 - - - +
132B LYS* 3.6 2.9 - - - -
133B VAL* 2.6 51.3 + - + +
134B ALA 4.9 1.1 - - - -
135B ASP* 3.2 54.9 + - + +
136B PRO* 4.8 4.3 - - - -
137B GLU* 5.8 1.2 + - - -
140B GLU* 1.3 74.1 - - - +
142B ALA* 1.3 59.9 + - - +
143B VAL* 3.9 1.3 - - + -
116F PHE* 3.6 4.1 - - - -
125F ASN* 3.2 30.5 + - - +
126F PHE* 4.6 2.8 - - - +
127F LYS* 6.1 0.2 - - - +
147F ASP* 2.8 49.8 + - - +
148F GLY* 3.1 18.2 + - - +
149F LYS* 3.8 8.0 - - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 4.5 7.9 - - + -
131B LYS 3.4 5.4 - - - +
140B GLU 4.3 0.8 + - - -
141B ARG* 1.3 72.3 - - - +
143B VAL* 1.3 61.2 + - - +
144B ILE* 3.9 3.1 - - + -
116F PHE* 3.4 22.6 - - + -
121F ILE* 3.5 38.2 - - + +
146F LEU 3.8 1.6 - - - +
147F ASP* 3.9 0.7 - - - -
148F GLY* 2.9 32.0 + - - +
150F TYR 4.4 1.4 - - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ASP* 3.6 4.7 - - - +
131B LYS* 2.9 42.8 + - + +
133B VAL* 3.9 24.2 - - + -
141B ARG* 5.2 1.6 - - + -
142B ALA* 1.3 74.4 - - - +
144B ILE* 1.3 60.7 + - - +
145B THR* 3.9 9.8 + - - +
145F THR* 3.5 31.9 - - + -
146F LEU 3.5 3.8 - - - +
147F ASP* 4.1 21.8 - - + +
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.3 40.4 - - + -
128B LEU* 5.5 0.4 - - + -
129B ASP 3.4 9.6 - - - +
130B VAL* 4.0 22.0 - - + -
142B ALA* 3.9 2.9 - - + -
143B VAL* 1.3 74.9 - - - +
145B THR* 1.3 62.6 + - - +
146B LEU* 4.0 25.1 - - + -
108F LEU* 4.8 12.1 - - + -
112F VAL* 5.7 0.4 - - + -
121F ILE* 4.2 25.4 - - + -
126F PHE* 6.5 0.7 - - + -
144F ILE 3.8 0.7 - - - +
145F THR* 3.6 1.4 - - - +
146F LEU* 2.7 56.8 + - + +
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LYS 4.3 0.5 - - - +
128B LEU* 3.6 4.9 - - - +
129B ASP* 3.1 49.6 + - - +
143B VAL* 3.9 14.6 + - - +
144B ILE* 1.3 76.3 + - - +
146B LEU* 1.3 71.3 + - - +
147B ASP* 4.1 5.8 + - + +
143F VAL* 3.5 31.9 - - + -
144F ILE 3.4 6.7 - - - +
145F THR* 4.1 7.8 + - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 6.6 0.2 - - + -
100B MET* 4.5 4.7 - - + -
108B LEU* 6.0 0.4 - - + -
121B ILE* 6.4 0.2 - - - -
126B PHE* 3.8 27.6 - - + -
128B LEU* 4.4 7.6 - - + -
144B ILE* 4.0 22.2 - - + -
145B THR* 1.3 75.8 - - - +
147B ASP* 1.3 58.0 + - - +
148B GLY 4.2 0.9 - - - -
97F PHE* 4.4 22.2 - - + -
100F MET* 3.9 33.2 - - + -
108F LEU* 6.0 0.2 - - + -
142F ALA 3.6 1.9 - - - +
143F VAL* 3.5 2.1 - - - -
144F ILE* 2.8 57.1 + - + +
146F LEU* 4.3 20.2 - - + -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 3.3 26.8 - - - -
127B LYS* 3.3 29.7 + - + +
145B THR* 5.1 6.1 - - + +
146B LEU* 1.3 72.7 - - - +
148B GLY* 1.3 58.4 + - - +
133F VAL* 5.8 0.2 - - - +
141F ARG* 2.8 41.7 + - - +
142F ALA 3.3 13.9 - - - +
143F VAL* 3.5 20.6 - - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.7 14.7 - - - +
122B ALA 3.5 11.9 - - - -
125B ASN 3.3 11.2 - - - -
126B PHE* 3.8 3.2 - - - -
146B LEU 4.2 0.6 - - - -
147B ASP* 1.3 76.0 + - - +
149B LYS* 1.3 61.2 - - - -
141F ARG* 3.3 9.4 - - - +
142F ALA* 2.8 32.7 + - - +
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.5 1.8 - - - -
122B ALA* 2.8 31.6 + - + +
125B ASN* 3.2 41.1 + - + +
148B GLY* 1.3 71.8 - - - -
150B TYR* 1.3 69.9 + - - +
151B LEU* 3.5 20.3 + - + +
135F ASP* 3.1 21.5 + - - +
138F GLY 3.4 25.8 + - - -
139F GLY* 4.2 3.3 - - - -
140F GLU 3.4 22.4 - - - +
141F ARG* 3.7 7.1 - - - +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 4.9 1.3 - - + -
116B PHE* 3.2 64.5 + + + -
117B GLY* 3.3 13.8 - - - -
118B ASP 2.7 30.4 + - - -
119B GLY* 4.2 2.9 - - - -
120B ILE 3.4 15.9 - - - -
121B ILE* 3.9 9.2 - - + -
148B GLY 3.8 2.0 + - - -
149B LYS* 1.3 80.8 - - - +
151B LEU* 1.3 71.0 + - - +
152B PRO* 3.5 30.2 - - + +
140F GLU* 2.9 41.2 + - + +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLY* 3.3 0.7 - - - -
120B ILE* 2.9 49.0 + - + +
122B ALA* 3.6 26.7 - - + -
125B ASN* 6.3 0.7 - - + -
149B LYS* 4.0 23.6 - - + +
150B TYR* 1.3 79.9 - - - +
152B PRO* 1.3 71.8 - - + +
122D ALA* 4.7 3.1 - - + -
124D ILE* 3.9 7.9 - - + +
125D ASN* 6.0 8.5 - - + +
151D LEU* 3.2 40.6 - - + -
1160F AZI 4.5 2.7 - - - +
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Residues in contact with PRO 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASP 3.4 6.1 - - - +
150B TYR* 3.5 37.0 - - + +
151B LEU* 1.3 90.7 - - + +
153B THR* 1.3 61.4 + - - +
154B LYS* 3.9 38.2 + - + +
124D ILE* 3.6 13.0 - - - +
125D ASN* 4.8 5.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il